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gatk3的最后一个经典版本3.8
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Scala 3.8%
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chartl 21ec44339d Somewhat major update. Changes: 
- ProduceBeagleInputWalker
 + Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present
 + Takes a bootstrap argument -- can use some given %age of the validation sites
 + Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap
-BeagleOutputToVCFWalker
 + Now filters sites where the genotypes have been reverted to hom ref
 + Now calls in to the new VCUtils to calculate AC/AN

-Queue
 + New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype
 + full calling pipeline v2 uses the above libraries
 + minor changes to some of my own scripts
 + no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-08 13:30:28 +00:00
R Better reporting -- figured out how to drop unused levels in subset 2010-10-06 14:31:51 +00:00
archive Cleaning up playground utils and tests 2010-08-27 01:25:47 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Somewhat major update. Changes: 2010-10-08 13:30:28 +00:00
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages /broad/1KG doesn't exist 2010-10-06 12:54:38 +00:00
perl update the example: /broad/1KG doesn't exist anymore 2010-10-05 13:50:24 +00:00
python File reports are now sorted in order 2010-10-06 21:54:23 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Somewhat major update. Changes: 2010-10-08 13:30:28 +00:00
settings Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. 2010-10-07 01:19:18 +00:00
shell Inprocess functions by default now log what output files they are running for. 2010-10-07 19:08:02 +00:00
testdata Fixes for example bam files 2010-10-05 18:43:02 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. 2010-10-07 01:19:18 +00:00
ivy.xml Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. 2010-10-07 01:19:18 +00:00